fix: copy header for ResampleImageBySpacing

Closes nipreps/niworkflows#459
nipy · Mar 2, 2020 · dffcb78 · dffcb78
1 parent dfe8501
commit dffcb78
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Showing 2 changed files with 15 additions and 0 deletions.
diff --git a/nipype/interfaces/ants/tests/test_auto_ResampleImageBySpacing.py b/nipype/interfaces/ants/tests/test_auto_ResampleImageBySpacing.py
@@ -7,6 +7,7 @@ def test_ResampleImageBySpacing_inputs():
         addvox=dict(argstr="%d", position=6, requires=["apply_smoothing"],),
         apply_smoothing=dict(argstr="%d", position=5,),
         args=dict(argstr="%s",),
+        copy_header=dict(mandatory=True, usedefault=True,),
         dimension=dict(argstr="%d", position=1, usedefault=True,),
         environ=dict(nohash=True, usedefault=True,),
         input_image=dict(argstr="%s", extensions=None, mandatory=True, position=2,),

diff --git a/nipype/interfaces/ants/utils.py b/nipype/interfaces/ants/utils.py
@@ -141,6 +141,12 @@ class _ResampleImageBySpacingInputSpec(ANTSCommandInputSpec):
     nn_interp = traits.Bool(
         argstr="%d", desc="nn interpolation", position=-1, requires=["addvox"]
     )
+    copy_header = traits.Bool(
+        True,
+        mandatory=True,
+        usedefault=True,
+        desc="copy headers of the original image into the output (corrected) file",
+    )
 
 
 class _ResampleImageBySpacingOutputSpec(TraitedSpec):
@@ -193,6 +199,14 @@ def _format_arg(self, name, trait_spec, value):
 
         return super(ResampleImageBySpacing, self)._format_arg(name, trait_spec, value)
 
+    def _list_outputs(self):
+        outputs = super(ResampleImageBySpacing, self)._list_outputs()
+        if self.inputs.copy_header:  # Fix headers
+            _copy_header(
+                self.inputs.input_image, outputs["output_image"], keep_dtype=True
+            )
+        return outputs
+
 
 class _ThresholdImageInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(